TCR / BCR profiling

Abstract

This disclosure relates to systems, methods, and compositions useful for profiling the T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. [Solution] This disclosure also relates to a system and method for diagnosing, treating or predicting infection, disease, medical condition, or treatment outcome or effect based on TCR / BCR profile data of a subject requiring such treatment.

Claims

1. a) Isolating RNA from patient samples, b) Enrich isolated RNA for TCR / BCR genes using a set of TCR / BCR hybrid capture probes, and enrich the targeted whole transcriptome panel using a set of hybrid capture probes. c) Determining the RNA sequence from (b) and generating sequencing data, d) Analyze sequencing data to determine the patient's TCR / BCR profile. A method for determining a patient's TCR / BCR profile, including, A method for assembling TCR / BCR hybrid capture probes comprising a first pool containing BCR steady-state region probes, a second pool containing BCR non-steady-state region probes, a third pool containing TCR steady-state region probes, a fourth pool containing TCR non-steady-state region probes, and a fifth pool containing transcriptome hybrid capture probes.

2. The method according to claim 1, wherein the ratio of the first pool to the second pool to the third pool to the fourth pool in the set is 1:2.5:100:

100.

3. The method according to claim 1, wherein the ratio of the first pool to the second pool to the third pool to the fourth pool to the fifth pool in the set is 1:2.5:100:100:

10.

4. The method according to claim 3, wherein less than 2% of the reads in the sequencing data are mapped to TCR / BCR genes.

5. The method according to claim 1, wherein step (c) comprises whole transcriptome sequencing or short-read sequencing.

6. The method according to claim 1, wherein step (d) includes identifying multiple TCR / BCR clones in the sample.

7. The method according to claim 1, wherein step (d) includes identifying the most abundant TCR / BCR clone in the sample.

8. The method according to claim 1, wherein step (d) includes identifying the most abundant non-stationary region sequence in the sample.

9. The method according to claim 1, wherein the sample is a blood sample or a solid tumor sample.

10. a) Isolating RNA from patient samples, b) Enrich isolated RNA for TCR / BCR genes using a TCR / BCR hybrid capture probe set, and enrich the targeted whole transcriptome panel using a transcriptome hybrid capture probe set. c) Determining the RNA sequence from (b) and generating sequencing data, d) Analyze sequencing data to determine the patient's TCR / BCR profile. A method for determining a patient's TCR / BCR profile, including, A method comprising a set of TCR / BCR hybrid capture probes comprising a first pool containing BCR constant region probes, a second pool containing BCR non-constant region probes, a third pool containing TCR constant region probes, and a fourth pool containing TCR non-constant region probes, wherein the ratio of transcriptome-targeted panel probes to the first pool, the second pool, the third pool, and the fourth pool in the set is 10:1:2.5:100:100, and less than 2% of reads in the sequencing data are mapped to TCR / BCR genes.

11. The method according to any one of claims 1 to 10, wherein step (c) comprises whole transcriptome sequencing or short-read sequencing.

12. The method according to any one of claims 1 to 11, comprising comparing a patient's BCR / TCR profile with a control TCR / BCR profile and, based on the comparison, identifying the patient as having a disease or medical condition.

13. The method according to claim 12, wherein the disease or condition is an infectious disease, cancer, autoimmune disease, or allergy.

14. The method according to claim 13, wherein the cancer or infectious disease is one or more of those listed in Embodiment 114.

15. The method according to any one of claims 1 to 11, wherein the analysis includes determining the presence or extent of lymphocyte infiltration in the tumor.

16. The method according to any one of claims 12 to 14, further comprising treating the patient with a therapeutic agent.

17. The method according to claim 16, wherein the therapeutic agent is an immunotherapy agent.

18. The method according to claim 17, wherein the immunotherapy agent is a vaccine.

19. The method according to claim 17, wherein the immunotherapy agent is a chimeric antigen receptor (CAR) T cell.

20. a) Isolating RNA from patient samples, b) Enrich isolated RNA for TCR / BCR genes using a set of TCR / BCR hybrid capture probes, and enrich the targeted whole transcriptome panel using a set of hybrid capture probes. c) Determining the RNA sequence from (b) and generating sequencing data, d) Analyzing sequencing data, the analysis including determining the most abundant TCR / BCR clone in the sample and, if applicable, determining the patient's TCR / BCR profile. The set of TCR / BCR hybrid capture probes includes a first pool containing BCR steady-state region probes, a second pool containing BCR non-steady-state region probes, a third pool containing TCR steady-state region probes, a fourth pool containing TCR non-steady-state region probes, and a fifth pool containing transcriptome hybrid capture probes, and (e) Treating the patient A method of treating a patient's disease or condition, including [specific example].

21. The method according to claim 20, wherein the ratio of the first pool to the second pool to the third pool to the fourth pool in the set is 1:2.5:100:

100.

22. The method according to claim 20, wherein the ratio of the first pool to the second pool to the third pool to the fourth pool to the fifth pool in the set is 1:2.5:100:100:

10.

23. The method according to claim 22, wherein less than 2% of the reads in the sequencing data are mapped to TCR / BCR genes.

24. The method according to claim 20, wherein the procedure comprises increasing the most abundant TCR / BCR clone in vitro and administering the increased clone to a patient.

25. The method according to claim 20, wherein step (d) comprises identifying the most abundant TCR non-stationary region sequence in the sample, and the treatment performed in step (e) comprises administering a CAR-T cell therapeutic agent, wherein the CAR-T cells comprise at least one of the most abundant TCR non-stationary region sequences.

26. a) At the first point in time before administering the drug, i) Isolating RNA from patient samples, ii) Enrich isolated RNA for TCR / BCR genes using a TCR / BCR hybrid capture probe set, and enrich the targeted whole transcriptome panel using a transcriptome hybrid capture probe set. iii) Determining the RNA sequence of (b) and generating sequencing data, and iv) Analyze sequencing data to determine the patient's TCR / BCR profile. b) At a second time point after the administration of the drug, i) Isolating RNA from patient samples, ii) Enrich isolated RNA for TCR / BCR genes using a TCR / BCR hybrid capture probe set, and enrich the targeted whole transcriptome panel using a transcriptome hybrid capture probe set. iii) Determining the RNA sequence of (b) and generating sequencing data, and iv) Analyze sequencing data to determine the patient's TCR / BCR profile, and c) Characterize the effect of treatment on the patient's TCR / BCR profile by comparing the TCR / BCR profile determined in step (a) with the TCR / BCR profile determined in step (b). A method for characterizing the effect of treatment on a patient's TCR / BCR profile, including, A method for assembling a set of hybrid capture probes, comprising a first pool containing TCR steady-state region probes, a second pool containing TCR transient region probes, a third pool containing BCR steady-state region probes, a fourth pool containing BCR transient region probes, and a fifth pool containing transcriptome hybrid capture probes.

27. The method according to claim 26, wherein the ratio of the first pool to the second pool to the third pool to the fourth pool in the set is 1:2.5:100:

100.

28. The method according to claim 27, wherein the ratio of the first pool to the second pool to the third pool to the fourth pool to the fifth pool in the set is 1:2.5:100:100:

10.

29. The method according to claim 28, wherein less than 2% of the reads in the sequencing data are mapped to TCR / BCR genes.

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